The term "proteomics" is rather new and is intended
to separate the science of understanding protein structure and function from genomics.
The proteome is constantly changing and interacting with
cells and other bio-molecules compared to a relatively stable genome.

Back to Basics

Polysaccharides, lipids and nucleic acids (DNA and RNA) are the
primary biological macromole-cules composing living organisms. Nucleotides are the
mono-mers of nucleic acids, which are composed of phosphate group, pentose sugar
and nitrogenous hetercyclous base (in DNA, purines include adenine and guanine while
pyrimidines include thymine and cytosine). DNA is a polymer of these nucleotides
encoding amino acids, and is often commonly referred to as the genetic code.

Amino acids, by definition, contain both an amino and carboxylic
acid attached to a shared carbon, and there are 20 standard amino acids that are
encoded (although many more amino acids have been identified, only two recently
identified are genetically encoded). Endogenous processes synthesize some amino
acids, while others are essential (they come from exogenous sources).

Finally, chains of amino acids form peptides, which in turn form
proteins. Proteins are essential to the structure and function of all living cells,
and are typically large molecules with masses up to 3,000,000 Daltons.

Assessing Proteins

A variety of methods exist to determine protein expression levels.
The first step typically involves separation, followed by identification, quantification
and sequencing. Traditional, gel-based methods in addition to SDS-PAGE and
immunological methods (western blot and surface-enhanced laser desorption and Ionization
[SELDI]) are still quite common for separation, but mass spectrometry has become
a practical method for the quantitation and simultaneous identification of complex
protein samples (such as those found in the tear film).

Proteins have many different functions. For example, many proteins
are enzymes, molecules that catalyze biochemical reactions and are commonly denoted
by terms ending in "-ase" preceded by the name of the molecule they modify (such
as matrix metalloproteinases in the tear film). Many diseases are associated with
over- or under-production of enzymes; researchers recently found that stimulation
matrix metalloproteinase-9 is associated with a decrease in epithelial barrier function
relating to dry eye and ocular surface desiccation.

Proteins also play structural and mechanical roles in the body.
An ophthalmic example includes proteoglycans, which are glycosylated proteins (chondroitin
sulfate) associated with collagen fibers in the corneal stroma. Collagen is known
for its tremendous tensile strength, as is the cornea.

Another main function of proteins is their role in the immune
response. For example, antibodies are proteins that help the body identify foreign
material. Immunoglobulins (IgG, IgA, IgM, IgD, IgE) are antibodies produced by B
cells of the humoral immune response. Portions of both IgG and IgM are associated
with the tear film, as are other immune-related proteins such as cytokines (interleukins),
tumor necrosis factor alpha and growth factors.

Pieces of the Puzzle

Proteins are important molecules to understand relative to unraveling
the etiology of dry eye disease. We are still learning much about not only the individual
proteins expressed in the tear film, but also their function and interaction with
other molecules such as lipids. A basic understanding of these issues will contribute
to developing new technologies and pharmaceutical strategies targeted toward treating
this disease.

Dr. Nichols is assistant
professor of optometry and vision science at The Ohio State University College of
Optometry. Dr. Green-Church is the director of the Mass Spectrometry and Proteomics
Facility at The Ohio State University.